At last report, Code Enforcement Officer Peter Wurster and Historic Preservation Chair Tom Swope had met with the owner and the contractor at 226-228 Warren Street and devised a way to bring the building into conformity with the plans that had been approved by the HPC. The remedy involves removing the roofs on the box windows, which had not been approved by the HPC, and adding a crown molding or cornice, which had been approved. According to Wurster, the end result will be a facade that is similar in appearance to the facade on 224 Warrren Street next door.
NOTE: I need to correct the previous paragraph and my previous post. In an email, Peter Wurster told me that he had spoken with Tom Swope, the contractor, and the owner. Foolishly and erroneously, I took that to mean that they had all been together in one place. What in fact happened, as Tom Swope has clarified in a comment and in a phone call to me, was that Wurster spoke with the contractor and the owner and reported the outcome to Swope. My apologies for misrepresenting that communication.
After studying the two buildings, it's not entirely clear how that similarity can be achieved. The problem may be that it is not possible to cobble together prefabricated elements, such as never existed in the 19th century, to make something that looks authentic and in character with the rest of the street.